Lecture 3A: Respiration Flashcards
Energy Production and Primary Metabolism
What is catabolism?
Breakdown of complex molecules
What do chemoorganotrophs obtain energy from?
Organic compounds
Organisms that obtain energy by oxidizing organic compounds and use them as both a source of energy and carbon are called __ (or __). Examples of organic compounds they utilize include: (4)
- chemoheterotrophs
- chemoorganotrophs
- Examples:
Carbohydrates (e.g., glucose, sucrose, starch)
Lipids (e.g., fatty acids, triglycerides)
Proteins (e.g., amino acids)
Nucleic acids (e.g., DNA, RNA components)
Fermentation occurs in the absence of what?
Oxygen
Does fermentation require an external electron acceptor?
No
What are the two types of respiration? (2)
Anaerobic and aerobic
What is the electron acceptor in aerobic respiration?
Oxygen
Give an example of an electron acceptor in anaerobic respiration. (2)
Nitrate (NO3^-) and sulfate (SO4^2-)
What is another name for glycolysis?
Embden-Meyerhof-Parnas pathway
What is glucose oxidized to in glycolysis?
Pyruvate
Is glycolysis found in both fermentation and respiration?
Yes
How many redox reactions occur in glycolysis?
Two
What type of phosphorylation produces ATP in glycolysis?
Substrate-level phosphorylation
What happens to pyruvate in respiration?
Further oxidized to CO₂
What happens to pyruvate in fermentation?
Used as an electron acceptor
What is the main electron acceptor in fermentation?
Internal organic molecules
What is the main electron acceptor in respiration?
External molecules (inorganic or organic)
Which pathway involves complete oxidation of the electron donor?
Respiration
What is the purpose of Stage I of glycolysis?
Prepare glucose for breakdown
Recite Glycolysis: Stage I: Preparatory Reactions (Energy Investment): Include the chemicals, chemical reactions, enzymes, ATP produced, and byproducts involved.
Glucose phosphorylation (first step):
- Reaction: Glucose → Glucose 6-phosphate
- Enzyme: Hexokinase (or Glucokinase in the liver)
- Use 1 ATP
Isomerization:
- Reaction: Glucose 6-phosphate → Fructose 6-phosphate
- Enzyme: Phosphoglucose isomerase
Phosphorylation of fructose 6-phosphate:
- Reaction: Fructose 6-phosphate → Fructose 1,6-bisphosphate
- Enzyme: Phosphofructokinase-1 (PFK-1)
- Use 1 ATP
Splitting of fructose 1,6-bisphosphate:
- Reaction: Fructose 1,6-bisphosphate → glyceraldehyde-3-phosphate (G3P) + Dihydroxyacetone phosphate (DHAP)
- Enzyme: Aldolase
Conversion of DHAP:
- Reaction: Dihydroxyacetone phosphate (DHAP) → glyceraldehyde-3-phosphate (G3P)
- Enzyme: Triose phosphate isomerase
What are the two products of fructose 1,6-bisphosphate splitting? (2)
- Dihydroxyacetone phosphate (DHAP)
- glyceraldehyde-3-phosphate (G3P)
Which molecule is Dihydroxyacetone phosphate (DHAP) converted into? Which enzyme catalyzes this reaction?
- glyceraldehyde-3-phosphate (G3P)
- Triosephosphate isomerase
How many ATP molecules are consumed in Stage I of glycolysis?
2 ATP
Do redox reactions occur in Stage I of glycolysis?
No
Recite Glycolysis: Stage II: Redox Reactions and ATP Production: Include the chemicals, chemical reactions, enzymes, ATP produced, and byproducts involved.
Oxidation of G3P:
- Reaction: G3P → 1,3-Bisphosphoglycerate (1,3-BPG)
- Enzyme: Glyceraldehyde-3-phosphate dehydrogenase
- Reduction: NAD⁺ → NADH
ATP Generation (First Substrate-Level Phosphorylation):
- Reaction: 1,3-Bisphosphoglycerate → 3-Phosphoglycerate
- Enzyme: Phosphoglycerate kinase
- ATP Produced: 1 ATP per G3P (2 ATP per glucose)
Isomerization Step:
- Reaction: 3-Phosphoglycerate → 2-Phosphoglycerate
- Enzyme: Phosphoglycerate mutase
Dehydration Reaction (Preparation for Final ATP Generation):
- Reaction: 2-Phosphoglycerate → Phosphoenolpyruvate (PEP)
- Enzyme: Enolase
- Byproduct: H₂O (water is removed)
ATP Generation (Second Substrate-Level Phosphorylation):
- Reaction: Phosphoenolpyruvate → Pyruvate
- Enzyme: Pyruvate kinase
- ATP Produced: 1 ATP per G3P (2 ATP per glucose)
How many ATP molecules are produced in Stage II of glycolysis?
4 ATP
What redox reaction occurs in Stage II of glycolysis?
NAD+ is reduced to NADH
NAD: Nicotinamide adenine dinucleotide
Recite Glycolysis: Stage III: Redox Balance and Fermentation: Include the chemicals, chemical reactions, enzymes, ATP produced, and byproducts involved. (Two types of fermentation)
Lactic Acid Fermentation (in animals and some bacteria)
- Reaction: Pyruvate → Lactate
- Enzyme: Lactate dehydrogenase
- Redox Balance: NADH → NAD⁺
Significance: Restores NAD⁺ for glycolysis, allowing ATP production to continue in the absence of oxygen
Alcoholic Fermentation (in yeast and some bacteria)
Step 1: Pyruvate → Acetaldehyde
- Enzyme: Pyruvate decarboxylase
- Byproduct: CO₂ (gas bubbles in alcoholic fermentation)
Step 2: Acetaldehyde → Ethanol
- Enzyme: Alcohol dehydrogenase
- Redox Balance: NADH → NAD⁺
What is the purpose of Stage III of glycolysis? (2)
- Regenerate NAD+
- Convert pyruvate into fermentation products under anaerobic conditions
Does Stage III of glycolysis produce net ATP?
No
What are two examples of fermentation products? (2)
Ethanol and lactate
What is the fermentation product of yeast?
Ethanol and CO2
What is the fermentation product of lactic acid bacteria?
Lactate
How many ATP are produced in glycolysis (net)?
2 ATP
How many NADH molecules are produced in glycolysis?
2 NADH
How many pyruvate molecules are produced per glucose?
2 Pyruvate
What are two common fermentable substrates? (2)
Sugars and polysaccharides
What must polysaccharides like starch and cellulose be broken down by?
Enzymes
What is the central metabolite in fermentation?
glucose
How are fermentations classified? (2)
By substrate or product formed
What fermentation pathway involves fatty acid products?
CoA derivative fermentation
Which bacterium ferments ethanol and acetate?
Clostridium kluyveri
What is the ecological role of fermentation? (1 general reason; 7 specific reasons)
Organic matter degradation in anoxic environments.
- Recycles nutrients (C, N, P, S) back into ecosystems
- Supports anaerobic microbial energy flow (alternative electron acceptors)
- Produces methane (CH₄) via methanogenesis (affects carbon cycle & greenhouse gases)
- Facilitates denitrification & sulfate reduction (reduces excess nitrate & sulfate)
- Used in bioremediation & waste treatment (anaerobic digesters, oil spill cleanup)
- Enables microbial survival in extreme environments (deep-sea vents, sediments)
- Essential for ecosystem stability and climate impact (methane emissions)
What are two common fermentation products used in food? (2)
Ethanol and lactic acid
What microorganism is used in baking and brewing?
Saccharomyces cerevisiae
What determines whether Saccharomyces cerevisiae ferments or respires?
Oxygen availability
Why does respiration yield more energy than fermentation?
Complete oxidation of glucose.
More info:
- Glucose is completely broken down into CO₂ and H₂O, releasing all its stored energy.
- In aerobic respiration, electrons from NADH & FADH₂ pass through the ETC, pumping protons to generate ATP via chemiosmosis.
- In fermentation, the ETC is not used, so NADH is recycled by converting pyruvate into lactate/ethanol, wasting potential ATP.
- Aerobic respiration: ~38 ATP per glucose
- Fermentation: Only 2 ATP per glucose
What enzyme converts pyruvate into Acetyl-CoA?
Pyruvate Dehydrogenase Complex (PDC)
What are the three key reactions in the transition step of pyruvate into Acetyl-CoA? (3)
1️⃣ Decarboxylation – Pyruvate (3C) → Acetyl group (2C) + CO₂
2️⃣ Oxidation – NAD⁺ → NADH
3️⃣ CoA attachment – Acetyl group + CoA → Acetyl-CoA
Where does the transition of pyruvate to Acetyl-CoA occur?
🧬 Mitochondrial matrix (eukaryotes)
🦠 Cytoplasm (prokaryotes)
Why is the transition step of pyruvate to Acetyl-CoA important?
✔ Links glycolysis to the Citric Acid Cycle
✔ Produces NADH for ATP generation
✔ Releases CO₂ (first carbon loss in respiration)
✔ Commits carbon to energy production or biosynthesis
Recite the Flow of the Citric Acid Cycle (Krebs Cycle) with Enzymes & Key Points
Acetyl-CoA + Oxaloacetate → Citrate
- Enzyme: Citrate synthase
- Key Point: First committed step; condensation reaction
Citrate → Isocitrate
- Enzyme: Aconitase
- Key Point: Isomerization via cis-aconitate intermediate
Isocitrate → α-Ketoglutarate
- Enzyme: Isocitrate dehydrogenase
Key Point:
- NAD⁺ → NADH (first redox reaction)
- CO₂ is released (first decarboxylation)
α-Ketoglutarate → Succinyl-CoA
- Enzyme: α-Ketoglutarate dehydrogenase
Key Point:
- NAD⁺ → NADH (second redox reaction)
- CO₂ is released (second decarboxylation)
Succinyl-CoA → Succinate
- Enzyme: Succinyl-CoA synthetase
Key Point:
- GDP + Pi → GTP (or ATP in some cells) (substrate-level phosphorylation)
Succinate → Fumarate
- Enzyme: Succinate dehydrogenase (Complex II of ETC)
- Key Point: FAD → FADH₂ (third redox reaction)
Fumarate → Malate
- Enzyme: Fumarase
- Key Point: Hydration reaction (adds H₂O)
Malate → Oxaloacetate
- Enzyme: Malate dehydrogenase
- Key Point: NAD⁺ → NADH (fourth redox reaction)
MNEMONICS: I Kiss Some Sexy Fucking Males On Campus
(Isocitrate, α-Ketoglutarate, Succinyl-CoA, Succinate, Fumarate, Malate, Oxaloacetate, Citrate)
What happens to pyruvate before entering the citric acid cycle?
It is decarboxylated to acetyl-CoA.
What molecule does acetyl-CoA combine with to form citrate?
Oxaloacetate
What are the key products of the citric acid cycle per 1 glucose?
- 6 CO₂
- 8 NADH
- 2 FADH₂
What happens to NADH and FADH₂ after the CAC?
They are oxidized in the electron transport chain (ETC) to produce ATP.
What are three key CAC intermediates used for biosynthesis? (3)
- α-Ketoglutarate
- oxaloacetate
- succinyl-CoA
What are CAC intermediates used to synthesize?
Amino acids, cytochromes, chlorophyll, and other biomolecules.
How is oxaloacetate replenished?
By carboxylation of pyruvate or phosphoenolpyruvate.
What is the function of the glyoxylate cycle?
Allows using C2 compounds (e.g., acetate) and replenishes oxaloacetate.
__ is a modified version of the Citric Acid Cycle that allows organisms (e.g., plants, bacteria, fungi) to convert __ (__) into __ by bypassing the __ steps of the Citric Acid Cycle.
- Glyoxyalate cycle
- acetate (Acetyl-CoA)
- glucose
- decarboxylation
What are the two key enzymes of the glyoxylate cycle? (2)
- Isocitrate lyase
- malate synthase
What reaction does isocitrate lyase catalyze?
Isocitrate → succinate + glyoxylate
What reaction does malate synthase catalyze?
Glyoxylate + acetyl-CoA → malate
Why is the glyoxylate cycle important?
It allows organisms to grow on acetate by bypassing decarboxylation steps of the CAC.
Recite the Glyoxylate cycle: Include the reactions and enzymes involved.
1️⃣ Acetyl-CoA + Oxaloacetate → Citrate
Enzyme: Citrate synthase
Reaction: Acetyl-CoA + Oxaloacetate + H₂O → Citrate + CoA
2️⃣ Citrate → Isocitrate
Enzyme: Aconitase
Reaction: Citrate → Isocitrate (via cis-aconitate intermediate)
3️⃣ Isocitrate → Succinate + Glyoxylate (Key Difference from TCA Cycle!)
Enzyme: Isocitrate lyase
Reaction: Isocitrate → Succinate + Glyoxylate
Key Point: Bypasses CO₂ release, preserving carbon for glucose synthesis
4️⃣ Glyoxylate + Acetyl-CoA → Malate
Enzyme: Malate synthase
Reaction: Glyoxylate + Acetyl-CoA + H₂O → Malate + CoA
5️⃣ Malate → Oxaloacetate
Enzyme: Malate dehydrogenase
Reaction: Malate + NAD⁺ → Oxaloacetate + NADH + H⁺
Oxidizes pyruvate to CO₂, generates NADH and FADH₂, and provides biosynthetic precursors.
Citric acid cycle
Replenishes oxaloacetate when growing on C2 compounds like acetate.
Glyoxylate cycle
Which pathway generates NADH and FADH₂ for ATP production?
Citric acid cycle
Which pathway allows growth on acetate?
Glyoxylate cycle
- How much ATP does aerobic respiration yield per glucose?
- How much ATP does fermentation yield per glucose?
~38 ATP
2 ATP
Tricarboxylic Acid Cycle
Which TCA intermediates serve as amino acid precursors? (2)
- α-Ketoglutarate
- oxaloacetate
- α-Ketoglutarate is a precursor for glutamate, which can be further converted into glutamine, proline, and arginine.
- Oxaloacetate is a precursor for aspartate, which can give rise to asparagine, methionine, lysine, and threonine.
Tricarboxylic Acid Cycle
What is succinyl-CoA needed for?
Formation of cytochromes, chlorophyll, and related molecules
Succinyl-CoA is essential for the biosynthesis of heme, which is a key component of cytochromes, chlorophyll, and related molecules.
Tricarboxylic Acid Cycle
How is oxaloacetate replenished if depleted?
By carboxylation of pyruvate or phosphoenolpyruvate (PEP) with CO₂
What role does oxaloacetate play in gluconeogenesis?
It can be converted into phosphoenolpyruvate (PEP), a glucose precursor
What molecule provides raw material for fatty acid biosynthesis?
Acetate
Glyoxylate Cycle
What C4 and C6 compounds can organisms use as electron donors? (4)
- Citrate
- malate
- fumarate
- succinate
Why can’t acetate be oxidized by the citric acid cycle alone?
The TCA cycle requires oxaloacetate regeneration, which can be depleted
Acetate cannot be oxidized by the citric acid cycle alone because the cycle requires a continuous supply of oxaloacetate to combine with acetyl-CoA and keep the cycle running.
* Acetate is converted into acetyl-CoA, which enters the TCA cycle by combining with oxaloacetate to form citrate.
* However, oxaloacetate can be depleted if it is diverted for biosynthetic pathways (e.g., amino acid synthesis or gluconeogenesis).
* Without sufficient oxaloacetate, acetyl-CoA cannot enter the cycle, leading to an accumulation of acetate-derived acetyl-CoA.
This is why organisms rely on anaplerotic reactions (e.g., pyruvate carboxylation) to replenish oxaloacetate and sustain the TCA cycle.
What is the key intermediate in the glyoxylate cycle?
What is the key intermediate in the glyoxylate cycle?
What happens to the succinate produced in the glyoxylate cycle?
It is used for biosynthesis
How is oxaloacetate produced from malate?
Through malate oxidation
Glyoxylate Cycle
What enzymes compensate for a shortage of C4 intermediates? (2)
- Pyruvate carboxylase
- phosphoenolpyruvate carboxylase
